X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=97e11eb05db197b43cb7ce699922e845e76aaf73;hb=331cf6c6db133ff63d426b8ab6ad6aed8f0e33c5;hp=af5a1fa929994dd7ef50a45a2f7817036dd329d0;hpb=449fb0be731c9283e9cad076a03fe730aeb2095a;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index af5a1fa..97e11eb 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -9,7 +9,7 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
-import jalview.structure.StructureViewSettings;
+import jalview.structure.StructureImportSettings;
 
 import java.awt.Color;
 import java.io.IOException;
@@ -67,19 +67,19 @@ public abstract class StructureFile extends AlignFile
 
   public void xferSettings()
   {
-    this.visibleChainAnnotation = StructureViewSettings
+    this.visibleChainAnnotation = StructureImportSettings
             .isVisibleChainAnnotation();
-    this.predictSecondaryStructure = StructureViewSettings
+    this.predictSecondaryStructure = StructureImportSettings
             .isPredictSecondaryStructure();
-    this.externalSecondaryStructure = StructureViewSettings
+    this.externalSecondaryStructure = StructureImportSettings
             .isExternalSecondaryStructure();
 
   }
 
-  public StructureFile(boolean parseImmediately, String inFile, String type)
+  public StructureFile(boolean parseImmediately, String dataObject, String type)
           throws IOException
   {
-    super(parseImmediately, inFile, type);
+    super(parseImmediately, dataObject, type);
   }
 
   public StructureFile(boolean a, FileParse fp) throws IOException
@@ -270,11 +270,11 @@ public abstract class StructureFile extends AlignFile
             predictSecondaryStructure, externalSecondaryStructure,
             new FileParse(getDataName(), type) };
 
-        StructureViewSettings.setShowSeqFeatures(false);
-        StructureViewSettings.setVisibleChainAnnotation(false);
-        StructureViewSettings
+        StructureImportSettings.setShowSeqFeatures(false);
+        StructureImportSettings.setVisibleChainAnnotation(false);
+        StructureImportSettings
                 .setPredictSecondaryStructure(predictSecondaryStructure);
-        StructureViewSettings
+        StructureImportSettings
                 .setExternalSecondaryStructure(externalSecondaryStructure);
         Object jmf = constructor.newInstance(args);
         AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
@@ -297,13 +297,14 @@ public abstract class StructureFile extends AlignFile
     } catch (ClassNotFoundException q)
     {
     }
+    StructureImportSettings.setShowSeqFeatures(true);
   }
 
   public PDBChain findChain(String id) throws Exception
   {
     for (PDBChain chain : getChains())
     {
-      if (chain.id.equalsIgnoreCase(id))
+      if (chain.id.equals(id))
       {
         return chain;
       }